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Information on EC 1.1.1.25 - shikimate dehydrogenase (NADP+) and Organism(s) Escherichia coli and UniProt Accession P15770

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EC Tree
IUBMB Comments
NAD+ cannot replace NADP+ . In higher organisms, this enzyme forms part of a multienzyme complex with EC 4.2.1.10, 3-dehydroquinate dehydratase . cf. EC 1.1.1.24, quinate/shikimate dehydrogenase (NAD+), EC 1.1.5.8, quinate/shikimate dehydrogenase (quinone), and EC 1.1.1.282, quinate/shikimate dehydrogenase [NAD(P)+].
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This record set is specific for:
Escherichia coli
UNIPROT: P15770
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Word Map
The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
shikimate dehydrogenase, skdh, sasdh, mtbsdh, shikimate 5-dehydrogenase, hpsdh, mtbsd, shikimate:nadp+ oxidoreductase, hi0607, tgsdh, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5-dehydroshikimate reductase
-
-
-
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5-dehydroshikimic reductase
-
-
-
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dehydroshikimic reductase
-
-
-
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DHS reductase
-
-
-
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NAD+-dependent enzyme quinate/shikimate dehydrogenase
-
quinate/shikimate dehydrogenase
-
shikimate 5-dehydrogenase
-
-
-
-
shikimate dehydrogenase
-
-
-
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shikimate oxidoreductase
-
-
-
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shikimate:NADP oxidoreductase
-
-
-
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shikimate:NADP+ 5-oxidoreductase
-
-
-
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shikimate:NADP+ oxidoreductase
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
-
-
-
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reduction
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
shikimate:NADP+ 3-oxidoreductase
NAD+ cannot replace NADP+ [3]. In higher organisms, this enzyme forms part of a multienzyme complex with EC 4.2.1.10, 3-dehydroquinate dehydratase [4]. cf. EC 1.1.1.24, quinate/shikimate dehydrogenase (NAD+), EC 1.1.5.8, quinate/shikimate dehydrogenase (quinone), and EC 1.1.1.282, quinate/shikimate dehydrogenase [NAD(P)+].
CAS REGISTRY NUMBER
COMMENTARY hide
9026-87-3
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
shikimate + NAD+
3-dehydroshikimate + NADH + H+
show the reaction diagram
-
-
-
r
shikimate + NADP+
3-dehydroshikimate + NADPH + H+
show the reaction diagram
L-quinate + NAD+
3-dehydroquinate + NADH + H+
show the reaction diagram
-
-
-
r
shikimate + NAD+
3-dehydroshikimate + NADH + H+
show the reaction diagram
-
-
-
r
shikimate + NADP+
3-dehydroshikimate + NADPH + H+
show the reaction diagram
additional information
?
-
usage of recombinant shikimate dehydrogenase as sensor reaction for determination of the cytosolic NADPH/NADP ratio in Saccharomyces cerevisiae, quantitative measurements of physiological variables in the cytosolic compartment by GC-MS/MS, cytosolic NADPH/NADP ratio in batch experiments, method, overview
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
shikimate + NAD+
3-dehydroshikimate + NADH + H+
show the reaction diagram
-
-
-
r
shikimate + NADP+
3-dehydroshikimate + NADPH + H+
show the reaction diagram
L-quinate + NAD+
3-dehydroquinate + NADH + H+
show the reaction diagram
-
-
-
r
shikimate + NAD+
3-dehydroshikimate + NADH + H+
show the reaction diagram
-
-
-
r
shikimate + NADP+
3-dehydroshikimate + NADPH + H+
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NADP+
NADPH
NADP+
NADPH
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(3R,3'R,4S,4'S,5R,5'R)-N,N'-(butane-1,4-diyl)bis(3,4,5-trihydroxycyclohex-1-ene-1-carboxamide)
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(3R,3'R,4S,4'S,5R,5'R)-N,N'-(ethane-1,2-diyl)bis(3,4,5-trihydroxycyclohex-1-ene-1-carboxamide)
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(3R,3'R,4S,4'S,5R,5'R)-N,N'-(propane-1,3-diyl)bis(3,4,5-trihydroxycyclohex-1-ene-1-carboxamide)
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(3R,4S,5R)-3,4,5-trihydroxy-N-(3-hydroxypropyl)cyclohex-1-ene-1-carboxamide
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(3R,4S,5R)-3,4,5-trihydroxy-N-(4-hydroxybutyl)cyclohex-1-ene-1-carboxamide
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(3R,4S,5R)-3,4,5-trihydroxy-N-(5-hydroxypentyl)cyclohex-1-ene-1-carboxamide
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(3R,4S,5R)-3,4,5-trihydroxy-N-(6-hydroxyhexyl)cyclohex-1-ene-1-carboxamide
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(3R,4S,5R)-3,4,5-tri[(tert-butyldimethylsilyl)oxy]cyclohex-1-enecarboxylic acid
-
additional information
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.13
shikimate
pH 9.0, 25°C, recombinant wild-type enzyme
0.056
NADP+
-
with shikimate, pH 9.0, 20°C
0.065
shikimate
-
with NADP+, pH 9.0, 20°C
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
190
shikimate
pH 9.0, 25°C, recombinant wild-type enzyme
237
NADP+
-
with shikimate, pH 9.0, 20°C
237
shikimate
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with NADP+, pH 9.0, 20°C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.42 - 16.72
NAD+
0.322 - 3200
NADP+
1461.5
shikimate
pH 9.0, 25°C, recombinant wild-type enzyme
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.458
(3R,3'R,4S,4'S,5R,5'R)-N,N'-(butane-1,4-diyl)bis(3,4,5-trihydroxycyclohex-1-ene-1-carboxamide)
potassium phosphate buffer, pH 7.5, 25°C, cofactor NADPH
0.416
(3R,3'R,4S,4'S,5R,5'R)-N,N'-(ethane-1,2-diyl)bis(3,4,5-trihydroxycyclohex-1-ene-1-carboxamide)
25°potassium phosphate buffer, pH 7.5, 25°C, cofactor NADPH
0.4
(3R,3'R,4S,4'S,5R,5'R)-N,N'-(propane-1,3-diyl)bis(3,4,5-trihydroxycyclohex-1-ene-1-carboxamide)
potassium phosphate buffer, pH 7.5, 25°C, cofactor NADPH
0.733
(3R,4S,5R)-3,4,5-trihydroxy-N-(3-hydroxypropyl)cyclohex-1-ene-1-carboxamide
potassium phosphate buffer, pH 7.5, 25°C, cofactor NADPH
0.717
(3R,4S,5R)-3,4,5-trihydroxy-N-(4-hydroxybutyl)cyclohex-1-ene-1-carboxamide
potassium phosphate buffer, pH 7.5, 25°C, cofactor NADPH
0.642
(3R,4S,5R)-3,4,5-trihydroxy-N-(5-hydroxypentyl)cyclohex-1-ene-1-carboxamide
potassium phosphate buffer, pH 7.5, 25°C, cofactor NADPH
0.587
(3R,4S,5R)-3,4,5-trihydroxy-N-(6-hydroxyhexyl)cyclohex-1-ene-1-carboxamide
potassium phosphate buffer, pH 7.5, 25°C, cofactor NADPH
additional information
additional information
-
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.652
(3R,3'R,4S,4'S,5R,5'R)-N,N'-(butane-1,4-diyl)bis(3,4,5-trihydroxycyclohex-1-ene-1-carboxamide)
Escherichia coli
potassium phosphate buffer, pH 7.5, 25°C, cofactor NADPH
0.588
(3R,3'R,4S,4'S,5R,5'R)-N,N'-(ethane-1,2-diyl)bis(3,4,5-trihydroxycyclohex-1-ene-1-carboxamide)
Escherichia coli
potassium phosphate buffer, pH 7.5, 25°C, cofactor NADPH
0.589
(3R,3'R,4S,4'S,5R,5'R)-N,N'-(propane-1,3-diyl)bis(3,4,5-trihydroxycyclohex-1-ene-1-carboxamide)
Escherichia coli
potassium phosphate buffer, pH 7.5, 25°C, cofactor NADPH
0.949
(3R,4S,5R)-3,4,5-trihydroxy-N-(3-hydroxypropyl)cyclohex-1-ene-1-carboxamide
Escherichia coli
potassium phosphate buffer, pH 7.5, 25°C, cofactor NADPH
0.882
(3R,4S,5R)-3,4,5-trihydroxy-N-(4-hydroxybutyl)cyclohex-1-ene-1-carboxamide
Escherichia coli
potassium phosphate buffer, pH 7.5, 25°C, cofactor NADPH
0.953
(3R,4S,5R)-3,4,5-trihydroxy-N-(5-hydroxypentyl)cyclohex-1-ene-1-carboxamide
Escherichia coli
potassium phosphate buffer, pH 7.5, 25°C, cofactor NADPH
0.829
(3R,4S,5R)-3,4,5-trihydroxy-N-(6-hydroxyhexyl)cyclohex-1-ene-1-carboxamide
Escherichia coli
potassium phosphate buffer, pH 7.5, 25°C, cofactor NADPH
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
19.9
pH 9.0, 25°C, recombinant enzyme
9.68
recombinant CEN.PK-aroE strain expressing the enzyme from Eschericha coli, pH 7.0, 25°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7
in vivo assay at
7.5
assay at, oxidation of NADPH
9
-
assay at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30
in vivo assay at
20
-
assay at
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
additional information
Escherichia coli strain PB12.SA22 and the derivatives ydiB- and ydiB+ are evaluated for their ability to produce shikimate (SA), quinate (QA), 3-dehydroshikimate (DHS), and 3-dehydroquinate (DHQ) in batch culture fermentations growing in 1-l fermentors using 500 ml of a mineral broth supplemented with 25 g/l glucose and 15 g/l YE. Biomass and glucose consumption and the production of aromatic intermediates of the SA pathway, SA, QA, DHQ, and DHS are determined for all derivatives, overview. The highest production of DHQ and DHS is 0.07 and 0.074 g/l, respectively. SA and QA are produced during the early exponential stage, as these compounds are detected during the first 5 h of cultivation (SA = 0.49 g/l and QA = 0.38 g/l, respectively). In the stationary stage and until 20 h of cultivation, this strain consumes the remaining residual glucose. From this time until the end of fermentation, the supernatant concentration of detected SA shows no significant changes, reaching 8.2 g/l by the end of fermentation (50 h), whereas the final QA concentration is 1.52 g/l
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
occurs only in the cytosol
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
in the ydiB knockout mutant, QA production is 6.17% relative to SA (mol/mol), indicating that the inactivation of ydiB is a suitable strategy to reduce QA production below 10% (mol/mol) relative to SA in culture fermentations for SA production. The inactivation of ydiB in Escherichia coli strain PB12.SA22 and the reduction in QA production support the role of YdiB in the synthesis of this compound from DHQ. In the absence of YdiB, the DHS concentration detected in supernatant cultures is maintained relatively constant during the stationary phase
metabolism
-
the enzyme catalyzes the fourth step of the shikimate pathway, a conserved biosynthetic route in plants, fungi, bacteria, and apicomplexan parasites
physiological function
-
shikimate dehydrogenase catalyzes the NADPH-dependent reduction of 3-deydroshikimate to shikimate, an essential reaction in the biosynthesis of the aromatic amino acids and a large number of other secondary metabolites in plants and microbes
additional information
modelling of steady state and dynamic fluxes into pentose phosphate pathway and the flux split ratio into glycolysis and pentose phosphate pathway in Saccharomyces recombinantly expressing Escherichia coli shikimate dehydrogenase, overview
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
29400
-
mass spectometry and calculation from DNA sequence
29410
-
mass spectrometry
29414
-
1 * 29414, mass spectrometry
32000
-
gel filtration, SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
additional information
-
structure analysis, dynamic light scattering measurements
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant enzyme, 20 mg/ml in 10 mM Tris-HCl, pH 7.6, 0.4 mM DTT, and 2.5 mM NADPH, 20°C, sitting-drop vapour-diffusion method, reservoir solution contains 1.65 M ammonium sulfate, 100 mM cacodylate buffer, pH 5.8, 1.5 ml of protein solution is mixed with an equal volume of reservoir solution, 10-12 days, cryoprotection with 20% v/v glycerol, X-ray diffraction structure determination and analysis at 2.3 A resolution
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
A243G
site-directed mutagenesis, the mutant shows altered cofactor specificity compared to wild-type enzyme
D195E
site-directed mutagenesis, the mutant shows altered cofactor specificity compared to wild-type enzyme
N149D
site-directed mutagenesis, the mutant shows altered cofactor specificity compared to wild-type enzyme
N149D/V152F
site-directed mutagenesis, the mutant shows altered cofactor specificity compared to wild-type enzyme
S131A
site-directed mutagenesis, the mutant shows altered cofactor specificity compared to wild-type enzyme
S131A/L135A
site-directed mutagenesis, the mutant shows altered cofactor specificity compared to wild-type enzyme
S131A/L135A/N149D/V152F
site-directed mutagenesis, the mutant shows altered cofactor specificity compared to wild-type enzyme
S131A/N149D/V152F
site-directed mutagenesis, the mutant shows altered cofactor specificity compared to wild-type enzyme
additional information
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, 50% glycerol, 1 mM benzamidine, 0.4 mM dithiothreitol
-
-20°C, Tris-HCl, pH 7.5, 0.4 mM DTT, 50% glycerol, long-term
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli by nickel affinity chromatography and dialysis
recombinant enzyme from aroE auxotrophic mutant strain AB2834 by ammonium sulfate fractionation, anion exchange chromatography, ultrafiltration, and gel filtration
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene aroE from Escherichia coli sstrain DH5alpha, recombinant overexpression in Saccharomyces cerevisiae strain CEN.PK 113-5D yielding strain CEN.PK-aroE
gene aroE, recombinant expression in Escherichia coli strain JM101
gene aroE, recombinant expression of His-tagged wild-type and mutant enzymes in Escherichia coli
gene aroE, overexpression in the aroE auxotrophic mutant strain AB2834
-
gene ydiB, the ydiB gene is cloned into plasmid pTOPO aroB aroE, resulting in the pTOPO ydiB aroB aroE derivative, enzyme overexpression in Escherichia coli strain PB12, quantitative RT-PCR analysis, coexpression of plasmid pTOPO aroB aroE and pJLB aroG fbr tktA and the cultivation of this derivative in Escherichia coli strain PB12.SA2 resulting in very high level expression of gene ydiB during exponential and stationary growth stages
overexpression in Escherichia coli K12
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
analysis
usage of Escherichia coli shikimate dehydrogenase as sensor reaction for determination of the cytosolic NADPH/NADP ratio in Saccharomyces cerevisiae, quantitative measurements of physiological variables in the cytosolic compartment by GC-MS/MS, cytosolic NADPH/NADP ratio in batch experiments, overview. The steady state sensor reaction based cytosolic free NADPH/NADP ratio is 15.6
drug development
-
the essential enzyme is a potential target for antimicrobials
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Chaudhuri, S.; Coggins, J.R.
The purification of shikimate dehydrogenase from Escherichia coli
Biochem. J.
226
217-223
1985
Escherichia coli
Manually annotated by BRENDA team
Yaniv, H.; Gilvarg, C.
Aromatic biosynthesis. XIV. 5-dehydroshikimic reductase
J. Biol. Chem.
213
787-795
1955
Escherichia coli
Manually annotated by BRENDA team
Maclean, J.; Campbell, S.A.; Pollock, K.; Chackrewarthy, S.; Coggins, J.R.; Lapthorn, A.J.
Crystallization and preliminary X-ray analysis of shikimate dehydrogenase from Escherichia coli
Acta Crystallogr. Sect. D
56
512-515
2000
Escherichia coli
Manually annotated by BRENDA team
Peek, J.; Christendat, D.
The shikimate dehydrogenase family: functional diversity within a conserved structural and mechanistic framework
Arch. Biochem. Biophys.
566
85-99
2015
Aquifex aeolicus (O67049), Arabidopsis thaliana (Q9SQT8), Archaeoglobus fulgidus (O27957), Archaeoglobus fulgidus ATCC 49558 (O27957), Aspergillus nidulans (P07547), Aspergillus nidulans FGSC A4 (P07547), Corynebacterium glutamicum (A4QB65), Escherichia coli, Helicobacter pylori, Mycobacterium tuberculosis, Populus trichocarpa, Pseudomonas putida (Q88IJ7), Pseudomonas putida KT 2240 (Q88IJ7), Staphylococcus aureus, Staphylococcus epidermidis (Q5HNV1), Staphylococcus epidermidis ATCC 35984 (Q5HNV1), Toxoplasma gondii (Q6W3D0)
Manually annotated by BRENDA team
Zhang, J.; ten Pierick, A.; van Rossum, H.M.; Seifar, R.M.; Ras, C.; Daran, J.M.; Heijnen, J.J.; Wahl, S.A.
Determination of the cytosolic NADPH/NADP ratio in Saccharomyces cerevisiae using shikimate dehydrogenase as sensor reaction
Sci. Rep.
5
12846
2015
Escherichia coli (P15770)
Manually annotated by BRENDA team
Diaz-Quiroz, D.C.; Cardona-Felix, C.S.; Viveros-Ceballos, J.L.; Reyes-Gonzalez, M.A.; Bolivar, F.; Ordonez, M.; Escalante, A.
Synthesis, biological activity and molecular modelling studies of shikimic acid derivatives as inhibitors of the shikimate dehydrogenase enzyme of Escherichia coli
J. Enzyme Inhib. Med. Chem.
33
397-404
2018
Escherichia coli (P15770), Escherichia coli
Manually annotated by BRENDA team
Garcia, S.; Flores, N.; De Anda, R.; Hernandez, G.; Gosset, G.; Bolivar, F.; Escalante, A.
The role of the ydiB gene, which encodes quinate/shikimate dehydrogenase, in the production of quinic, dehydroshikimic and shikimic acids in a PTS-strain of Escherichia coli
J. Mol. Microbiol. Biotechnol.
27
11-21
2017
Escherichia coli (P0A6D5), Escherichia coli PB12 (P0A6D5)
Manually annotated by BRENDA team
Garcia-Guevara, F.; Bravo, I.; Martinez-Anaya, C.; Segovia, L.
Cofactor specificity switch in shikimate dehydrogenase by rational design and consensus engineering
Protein Eng. Des. Sel.
30
533-541
2017
Escherichia coli (P15770), Escherichia coli
Manually annotated by BRENDA team